Metadata-Version: 2.1
Name: clinical-variant-ark
Version: 4.1.2
Summary: A Python client for the Clinical Variant Ark
Home-page: https://github.com/genomicsengland/pyark
Author: ['Pablo Riesgo Ferreiro', 'Kevin Savage', 'William Bellamy']
Author-email: pablo.riesgo-ferreiro@genomicsengland.co.uk
License: Apache
Download-URL: https://github.com/genomicsengland/pyark/archive/v4.1.2.tar.gz
Description: # pyark
        
        pyark is a python client to the Clinical Variant Ark (CVA) REST API 
        [https://github.com/genomicsengland/clinical_variant_ark](https://github.com/genomicsengland/clinical_variant_ark).
        pyark primary aim is to facilitate access to CVA knowledge base hiding the complexity using the REST API. 
        Also by integrating with major Python data analysis libraries it aims at enabling an analytical framework on CVA.
        
        ## Getting Started
        
        ### Prerequisites
        
        pyark works with python 2.7 up to python 3.6.
        
        ### Installing
        
        Install with pip:
        
        ```
        pip install clinical-variant-ark
        ```
        
        You will need a CVA server up and running and you will need credentials with the right authorisation permissions.
        
        Initialise the client:
        ```python
        from pyark.cva_client import CvaClient
        
        cva = CvaClient(url_base="https://your.cva", user="you", password="your_secret")
        cases_client = cva.cases()
        pedigrees_client = cva.pedigrees()
        entities_client = cva.entities()
        variants_client = cva.variants()
        report_events_client = cva.report_events()
        transactions_client = cva.transactions()
        ```
        
        Query CVA's knowledge base:
        ```python
        cases_client.count()
        ```
        
        Check the version of the client you are using:
        ```python
        import pyark
        
        print("pyark version {}".format(pyark.VERSION))
        ```
        
        See the documentation for further usage at [https://genomicsengland.github.io/pyark/](https://genomicsengland.github.io/pyark/).
        
        ## Running the tests
        
        Set the following environment variables:
        ```bash
        export CVA_URL_BASE="https://your.cva"
        export CVA_USER="you"
        export CVA_PASSWORD="your_secret"
        ```
        
        Then run unit tests:
        ```bash
        python -m unittest discover
        ```
        
        These tests rely on a working CVA server with some data in it.
        
        ## Versioning
        
        We use [semantic versioning](http://semver.org/). The major and minor versions are aligned with the CVA backend versioning. 
        
        ## Authors
        
        * **Pablo Riesgo Ferreiro** [priesgo](https://github.com/priesgo)
        * **Kevin Savage** [kevinpetersavage](https://github.com/kevinpetersavage)
        * **William Bellamy** [squinker](https://github.com/squinker)
        
        See also the list of [contributors](https://github.com/genomicsengland/pyark/contributors) who participated in this project.
        
        ## License
        
        This project is licensed under the Apache v2.0 license - see the [LICENSE.md](LICENSE.md) file for details
        
        ## Acknowledgments
        
        * Genomics England bioinformatics team as an infinite source of requirements
        * Katherine Smith and Augusto Rendon for spending their time playing with pyark!
        * Antonio Rueda Martin for listening to us
        
Keywords: CVA,pyark,clinical variant ark,Genomics England
Platform: UNKNOWN
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Healthcare Industry
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: Apache Software License
Classifier: Programming Language :: Python :: 2.7
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Description-Content-Type: text/markdown
Provides-Extra: test
